You can do very well believing "a calorie is a calorie" even if it is technically inaccurate, and you can do very badly believing "not all calories are created equal" even if it is technically true on some level.
Effective weight loss is simple (note I didn't say "easy"):
- Calculate your TDEE. TDEE is ((RMR + TEF + NEAT) * Physical Activity Level).
- Eat fewer calories than your TDEE in order to lose body fat or eat more to gain body fat.
- Most of the population are Sedentary or Moderately active. Many also overestimate their PAL by one level (i.e. you aren't "Vigorously" because you hit the gym twice this week for 20 minutes, you're Moderately).
- Exercise to improve overall health (mental, sleep, immune system, etc). Don't "double count" exercise calories, just set your PAL level and that's it.
- Don't eat less than 1500 / 1300 calories for men / women respectively and try to get some nutrients.
Ignore everything else, it is just adding complexity. Weight loss should be "Simple but hard." "Complex but easy" doesn't exist unfortunately, at least not in the medium to long term. Instead, you'll just burn out faster. So K.I.S.S., make it boring, make it a habit, eat whatever you want below your TDEE.
PS - Starting new exercise (or periods in women) can cause short term water weight increases in the order of 1-6 lbs. This is caused by inflammation. It is completely normal and will go away on its own. Just be patient.